This is a wild guess but I had a smililar problem a while back and in my case it was due to permissions for the user is being used to run the scheduled job.
Try setting a specific user in the code, preferably an admin account, and see if this solves the issue.

I actually went down that path too based on something a co-worker told me based on how the scheduled tasks run, but unfortunately that was not the issue, still do not get the one catalog back.

Still was unable to get anything to get it back correctly, so I ended up coding this out to meet my needs:

var languageBranch = _languageBranch.Service.ListEnabled();
var catalogList = new List<CatalogContent>();

foreach (var lang in languageBranch) {
    var catList = _contentLoader.Service.GetChildren<CatalogContent>(_referenceConverter.Service.GetRootLink(), new LanguageSelector(lang.LanguageID))   

    foreach(var catTemp in catList)
   {
        if (!catalogList.Exists(x => x.CatalogId == catTemp.CatalogId))
       {
            catalogList.Add(catTemp);
        }
    }
}

This meets my needs, but it still doesn't make sense as to why my original code wasn't bringing back the one catalog that didn't have en-us as an available language.

What is set as the master language?

For making the content loader fall back to a specific language you could do

var fallbackCulture = new CultureInfo("en-US");

_contentLoader.Service.GetChildren<CatalogContent>(_referenceConverter.Service.GetRootLink(), new LoaderOptions() { LanguageLoaderOption.FallbackWithMaster(fallbackCulture) });

Or always fetch from master language

_contentLoader.Service.GetChildren<CatalogContent>(_referenceConverter.Service.GetRootLink(), new LoaderOptions() { LanguageLoaderOption.MasterLanguage() });

I guess really the net issue I was trying to solve is how come this:

var catalogs = _contentLoader.GetChildren<CatalogContent>(_referenceConverter.GetRootLink());

Doesn't correctly return me all catalogs as it should.  

That being said, in response to the previouse comment, our master language is en-us, so setting the master language would still not get us back catalog C with languages of en-ca and fr-ca.

LanguageSelector.AutoDetect(true)

Try using this as language selector...

Is catalog Enabled?

It sure is.

I was haveing the same issue. 

Instead of using IContentLoader use IContentRepository. 

Not working 

var catalogs1 = _contentLoader.GetChildren<CatalogContent>(catalogRootLink);

Working

var catalogs = _contentRepository.GetChildren<CatalogContent>(catalogRootLink);

@David I doubt that was the problem. IContentRepository actually extends IContentLoader.

Make sure you don't make the same mistake I did: https://vimvq1987.com/beware-icontentloader-getchildren/ 

@Quan I can't speak to the problem anymore as my post was from almost 2-years ago. :)

I know, I was replying to David Fewless :) 

As always, it might benefit the future visitors